Lake City is a city in Goodhue and Wabasha counties in the U.S. state of Minnesota. It lies along Lake Pepin, a wide portion of the Mississippi …Lake City is a city in Goodhue and Wabasha counties in the U.S. state of Minnesota. It lies along Lake Pepin, a wide portion of the Mississippi River. The population was 5,252 at the 2020 census. Most of Lake City is located within Wabasha County with only a small portion in Goodhue County. Lake City is part of the Rochester, Minnesota Metropolitan Statistical Area.